Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PGR

Cell type

Cell type Class
Uterus
Cell type
Ishikawa
Primary Tissue
Uterus
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
endometrial adenocarcinoma
disease state
endometrial adenocarcinoma
cell line
Ishikawa
cell modification
none
passages
20-26
cell type
epithelial-like
growth mode
adherent
chip antibody
PR H190 (Santa Cruz)
treatment
PR-immunoprecipitated DNA from 5min R5020-treated cells

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were incubated in 1% Formaldehyde for 10min at 37ºC. After quenching with glycine, cells were whased once in ice cold PBS and collected in PBS plus protease and phosphatase inhibitors using a scrapper. Cells were lysed in two secuential steps to release nuclear contet and inmediately sonicated in Bioruptor. Sonication was evaluated by agarose gel electrophoresis, considering it succesful when fragments were homogenously distrubuted between 200-400bp. Enrichment of receptor-bound DNA was achieved by incubation with specific antibodies against either PR or ERalfa and immunoprecipitation with protein A beads. Libraries were prepared by the Genomics unit of the CRG Core Facility (Centre for Genomic Regulation, Barcelona, Spain) with NEBNext® ChIP-Seq Library Prep Reagent Set (ref. E6200S Illumina). Libraries were quality checked and quantified for single-end sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
54497436
Reads aligned (%)
97.4
Duplicates removed (%)
9.3
Number of peaks
1664 (qval < 1E-05)

hg19

Number of total reads
54497436
Reads aligned (%)
96.6
Duplicates removed (%)
11.3
Number of peaks
1594 (qval < 1E-05)

Base call quality data from DBCLS SRA